Two faces inside of each other sharing same 4 vertices, why and how to fix?
Ok. I got it to work by doing this:

Select all &gt; Mesh &gt; Split &gt; Faces by Edges
Merge by distance
Recalculate outside (just to be safe)

Though I'm still not sure exactly what was going on, there were obviously a great number of duplicate SOMETHING because the merge by distance operation after the edge-split removed 8743 vertices.
I suspect that the fill-holes operation ( on whatever you had selected when you performed it) created faces that were SOMEWHERE? (I give pause here because up until now, I believed it impossible for blender to define 2 faces with the same verts and edges in the same place - if anyone can clarify further, It would be very informative, and I would be very curious to know how this works).
The only way I can conceive of this happening is that there could be 2 faces on top of one another with their normals facing opposite ways, however this theory is negated by the normal's directions themselves as seen in the images below:


Regardless, the &quot;faces-on-faces&quot; theory still has some merit, because that's the only way I can explain an edge split followed by a merge by distance working the way it did. The only other POSSIBLE thing I can think of is that somehow, some faces got &quot;folded back on themselves&quot;, creating the ultimate 180 degree non-manifold plane (sounds weirder the more that I think about it).
Either way, my guess is this is likely the result of a fill-holes operation on to many conjoined faces at once. That's the best I can do. Anyone who knows more about how this type of situation can come about is welcome to explain it further.
Here is an updated .blend with the result of the operations (however they worked)